YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|169890862, gi...
Organism:	Escherichia coli str. K-12 substr. DH10B
Length:	274 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|169890862, gi....

Description	E-value	Query Range	Subject Range
gi\|11992160 - gi\|11992160\|gb\|AAG42472.1\|AF311305_1 transcriptional regulator GadY [Escherichia coli] GADX_ECO27 - HTH-type transcriptional regulator gadX OS=Escherichia coli O127:H6 GN=gadX PE=2 SV=1 GADX_ECO27 - HTH-type transcriptional regulator GadX OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=gadX...	181.0	[0..1]	[274..1]
GADX_ECOL6 - HTH-type transcriptional regulator gadX OS=Escherichia coli O6 GN=gadX PE=2 SV=1 gi\|91074596, gi\|... - gi\|91213022\|ref\|YP_543008.1\| DNA-binding transcriptional regulator GadX [Escherichia coli UTI89], gi... gi\|226902547, gi... - gi\|237703283\|ref\|ZP_04533764.1\| transcriptional regulator gadX [Escherichia sp. 3_2_53FAA], gi\|22690... GADX_ECOL6 - HTH-type transcriptional regulator GadX OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPE... gi\|227839554, gi... - gi\|227883675\|ref\|ZP_04001480.1\| DNA-binding transcriptional regulator GadX [Escherichia coli 83972],... gi\|117625799, gi... - gi\|117625799\|ref\|YP_859122.1\| DNA-binding transcriptional regulator GadX [Escherichia coli APEC O1],...	180.0	[0..1]	[274..1]
gi\|191170413, gi... - gi\|191170413\|ref\|ZP_03031966.1\| transcriptional regulator GadX [Escherichia coli F11], gi\|190909221\|... gi\|110345354, gi... - gi\|110643762\|ref\|YP_671492.1\| DNA-binding transcriptional regulator GadX [Escherichia coli 536], gi\|...	179.0	[0..1]	[274..1]
gi\|82545880, gi\|... - gi\|82545880\|ref\|YP_409827.1\| DNA-binding transcriptional regulator GadX [Shigella boydii Sb227], gi\|... gi\|218697225, gi... - gi\|218697225\|ref\|YP_002404892.1\| DNA-binding transcriptional regulator GadX [Escherichia coli 55989]... gi\|218556066, gi... - gi\|218556066\|ref\|YP_002388979.1\| DNA-binding transcriptional regulator GadX [Escherichia coli IAI1],... gi\|209914235, gi... - gi\|209920976\|ref\|YP_002295060.1\| DNA-binding transcriptional regulator GadX [Escherichia coli SE11],... gi\|194428671, gi... - gi\|194428671\|ref\|ZP_03061208.1\| transcriptional regulator GadX [Escherichia coli B171], gi\|194413254... gi\|192958151, gi... - gi\|193068500\|ref\|ZP_03049462.1\| transcriptional regulator GadX [Escherichia coli E110019], gi\|192958... gi\|193061658, gi... - gi\|193061658\|ref\|ZP_03042755.1\| transcriptional regulator GadX [Escherichia coli E22], gi\|192932448\|... gi\|191165288, gi... - gi\|191165288\|ref\|ZP_03027131.1\| transcriptional regulator GadX [Escherichia coli B7A], gi\|190904690\|... gi\|187730117, gi... - gi\|187730117\|ref\|YP_001882202.1\| transcriptional regulator GadX [Shigella boydii CDC 3083-94], gi\|18... gi\|157157443, gi... - gi\|157157443\|ref\|YP_001464986.1\| DNA-binding transcriptional regulator GadX [Escherichia coli E24377... gi\|74313938, gi\|... - gi\|74313938\|ref\|YP_312357.1\| DNA-binding transcriptional regulator GadX [Shigella sonnei Ss046], gi\|...	174.0	[0..1]	[274..1]
GADX_SHIFL - HTH-type transcriptional regulator GadX OS=Shigella flexneri GN=gadX PE=3 SV=1 gi\|24054060, gi\|... - gi\|24114829\|ref\|NP_709339.1\| DNA-binding transcriptional regulator GadX [Shigella flexneri 2a str. 3... gi\|30065159, gi\|... - gi\|30065159\|ref\|NP_839330.1\| DNA-binding transcriptional regulator GadX [Shigella flexneri 2a str. 2...	172.0	[0..1]	[274..1]
gi\|110617326, gi... - gi\|110807778\|ref\|YP_691298.1\| DNA-binding transcriptional regulator GadX [Shigella flexneri 5 str. 8...	172.0	[0..1]	[274..1]
gi\|189369501, gi... - gi\|189369501\|gb\|EDU87917.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4501], g... gi\|168765923, gi... - gi\|189364822\|gb\|EDU83241.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4486], g... gi\|209755556, gi... - pir\|\|E86024 probable ARAC-type regulatory protein yhiX [imported] - Escherichia coli (strain O157:H7... gi\|168772530, gi... - gi\|187771509\|gb\|EDU35353.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4196], g... gi\|168779659, gi... - gi\|189002276\|gb\|EDU71262.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4076], g... gi\|12518228, gi\|... - gi\|15804060\|ref\|NP_290096.1\| DNA-binding transcriptional regulator GadX [Escherichia coli O157:H7 ED... gi\|188018486, gi... - gi\|188018486\|gb\|EDU56608.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4113], g... gi\|168753328, gi... - gi\|189359386\|gb\|EDU77805.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4401], g... GADX_ECO57 - HTH-type transcriptional regulator GadX OS=Escherichia coli O157:H7 GN=gadX PE=3 SV=1 gi\|254594869, gi... - gi\|254795469\|ref\|YP_003080306.1\| DNA-binding transcriptional dual regulator [Escherichia coli O157:H... gi\|208735755, gi... - gi\|208814478\|ref\|ZP_03255807.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4045... gi\|208819839, gi... - gi\|208819839\|ref\|ZP_03260159.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4042... gi\|209159511, gi... - gi\|209398111\|ref\|YP_002272993.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC411... gi\|217324900, gi... - gi\|217324900\|ref\|ZP_03440984.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. TW1458... gi\|168785381, gi... - gi\|189374307\|gb\|EDU92723.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC869], gi... gi\|189379897, gi... - gi\|189379897\|gb\|EDU98313.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC508], gi... gi\|195935044 - gi\|195935044\|ref\|ZP_03080426.1\| DNA-binding transcriptional regulator GadX [Escherichia coli O157:H7... gi\|15833650, gi\|... - gi\|15833650\|ref\|NP_312423.1\| DNA-binding transcriptional regulator GadX [Escherichia coli O157:H7 st... gi\|208726265, gi... - gi\|208806464\|ref\|ZP_03248801.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4206...	171.0	[0..1]	[274..1]
gi\|82778652, gi\|... - gi\|82778652\|ref\|YP_405001.1\| DNA-binding transcriptional regulator GadX [Shigella dysenteriae Sd197]...	167.0	[0..1]	[274..1]
gi\|50590983, gi\|... - gi\|81097031\|ref\|ZP_00875347.1\| Helix-turn-helix, AraC type:Arac protein, arabinose-binding/dimerisat...	163.0	[0..2]	[246..35]
gi\|71279582, gi\|... - gi\|71279582\|ref\|YP_269560.1\| AraC family substrate binding transcriptional regulator [Colwellia psyc...	163.0	[0..3]	[243..35]

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Predicted Domain #1

Region A:
Residues: [1-138]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQSLHGNCLI AYARHKYILT MVNGEYRYFN GGDLVFADAS QIRVDKCVEN FVFVSRDTLS  60
   61 LFLPMLKEEA LNLHAHKKVS SLLVHHCSRD IPVFQEVAQL SQNKNLRYAE MLRKRALIFA 120
  121 LLSVFLEDEH FIPLLLNV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.69897
Match:	2arcA
Description:	Regulatory protein AraC
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [139-274]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LQPNMRTRVC TVINNNIAHE WTLARIASEL LMSPSLLKKK LREEETSYSQ LLTECRMQRA  60
   61 LQLIVIHGFS IKRVAVSCGY HSVSYFIYVF RNYYGMTPTE YQERSAQRLS NRDSAASIVA 120
  121 QGNFYGTDRS AEGIRL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	20.0
Match:	1d5yA
Description:	Rob transcription factor, N-terminal domain; Rob transcription factor, C-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.57523737355937	bayes_pls_golite062009
DNA binding	2.7565055095762	bayes_pls_golite062009
nucleic acid binding	2.48097584527739	bayes_pls_golite062009
transcription factor activity	2.33198016659192	bayes_pls_golite062009
binding	2.21133851845856	bayes_pls_golite062009
sequence-specific DNA binding	0.37638337609693	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.24108783215685	bayes_pls_golite062009
transcription repressor activity	0.20862059645422	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: